[R-sig-Geo] raster pkg: overwriting the dimensions detected by netcdf4 (PERSIANN-CDR)

MAURICIO ZAMBRANO BIGIARINI mauricio.zambrano at ufrontera.cl
Wed Feb 3 16:20:36 CET 2016


On 3 February 2016 at 11:34, Michael Sumner <mdsumner at gmail.com> wrote:
>
>
> On Thu, 4 Feb 2016 at 01:26 MAURICIO ZAMBRANO BIGIARINI
> <mauricio.zambrano at ufrontera.cl> wrote:
>>
>> Dear spatial community,
>>
>> While reading some netCDFfiles with the raster package , I got a
>> "rotated" file, where the columns where read as rows and vice versa:
>>
>> ------------- START ----------------
>> x <- raster("PERSIANN-CDR_v01r01_20090101_c20140523.nc")
>> Loading required namespace: ncdf4
>> plot(x)
>> x
>> class       : RasterLayer
>> dimensions  : 1440, 480, 691200  (nrow, ncol, ncell)
>> resolution  : 0.25, 0.25  (x, y)
>> extent      : -60, 60, 0, 360  (xmin, xmax, ymin, ymax)
>> coord. ref. : NA
>> data source : /home/hzambran/PERSIANN-CDR_v01r01_20090101_c20140523.nc
>> names       : NOAA.Climate.Data.Record.of.PERSIANN.CDR.daily.precipitation
>> z-value     : 2009-01-01
>> zvar        : precipitation
>> ------------- END ----------------
>>
>
> Transpose might be sufficient?
>
> tx <- t(x)
>
> plot(tx)
> tx


Thanks Michale,

In fact, that is what I'm doing for reading the files, and the spatial
extent is correct and the precipitation values also seems to be right.

However, my question was more "conceptual", in the sense that the
provider says that the original file is NOT rotated, while the only
way  I have to get the correct files is rotating the original file
with the 't' command you mentioned.

In addition, while reading the file with the latest version of GRASS
GIS (7.0.3), and I got the following error message:

"
(Tue Feb  2 19:41:29 2016)
r.in.gdal input=/home/hzambran/PERSIANN-CDR_v01r01_20090101_c20140523.nc
output=PERSIANN_CDR_v01r01_20090101_c20140523 -e
Warning 1: dimension #2 (lat) is not a Longitude/X
dimension.
Warning 1: dimension #1 (lon) is not a Latitude/Y dimension.
ERROR: Input raster map is flipped or rotated - cannot import. You may
use 'gdalwarp' to transform the map to North-up.
"


So, I'm quite sure that the original file IS rotated, but I didn't
have more technical arguments to give to the data provider to
demonstrate that the file is rotated, because they insist that the
rotation is because R is not reading the file in the proper way....

mzb

=====================================
"In the end, it's not the years in your life that count.
 It's the life in your years". (Abraham Lincoln)
=====================================
Linux user #454569 -- Linux Mint user

>> 60W-60E and 0-360N, while the correct extent should be: 60S, 60N, 0E,
>> 360E.
>>
>> The file can be downloaded from:
>>
>> ftp://data.ncdc.noaa.gov/cdr/persiann/files/2009/PERSIANN-CDR_v01r01_20090101_c20140523.nc
>>
>>
>> After contacting the providers of the file, they mentioned that when
>> reading the file I have to provide the dimension information, i.e.,
>> 480 rows and 1440 columns, while the raster package detects the other
>> way around.
>>
>> I would highly appreciate if you could tell me:
>>
>> 1) is the previous situation a bug of my netCDF driver (netCDF 4.1.3,
>> GDAL 1.11.2, released 2015/02/10) or a problem of the dimensions
>> actually recorded in the netCDF file ?
>>
>> 2) is there any way to  overwrite the dimensions detected by netcdf4
>> when reading the file with the 'raster' command ?
>>
>>
>> My sessionInfo():
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 14.04.2 LTS
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] raster_2.5-2 sp_1.2-1
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.2.3     Rcpp_0.12.3     ncdf4_1.15      grid_3.2.3
>> [5] lattice_0.20-33
>>
>>
>> Thanks in advance and kind regards
>>
>> Mauricio Zambrano-Bigiarini, PhD
>>
>> =====================================
>> Dept. of Civil Engineering
>> Faculty of Engineering and Sciences
>> Universidad de La Frontera
>> PO Box 54-D, Temuco, Chile
>> http://ingenieriacivil.ufro.cl/
>> =====================================
>> mailto     : mauricio.zambrano at ufrontera.cl
>> work-phone : +56 45 259 2812
>> =====================================
>> "In the end, it's not the years in your life that count.
>>  It's the life in your years". (Abraham Lincoln)
>> =====================================
>> Linux user #454569 -- Linux Mint user
>>
>> --
>> La información contenida en este correo electrónico y cualquier anexo o
>> respuesta relacionada, puede contener datos e información confidencial y
>> no
>> puede ser usada o difundida por personas distintas a su(s)
>> destinatario(s).
>> Si usted no es el destinatario de esta comunicación, le informamos que
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>> un delito conforme a la ley chilena. Si lo ha recibido por error, por
>> favor
>> borre el mensaje y todos sus anexos y notifique al remitente.
>>
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>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>

-- 
La información contenida en este correo electrónico y cualquier anexo o 
respuesta relacionada, puede contener datos e información confidencial y no 
puede ser usada o difundida por personas distintas a su(s) destinatario(s). 
Si usted no es el destinatario de esta comunicación, le informamos que 
cualquier divulgación, distribución o copia de esta información constituye 
un delito conforme a la ley chilena. Si lo ha recibido por error, por favor 
borre el mensaje y todos sus anexos y notifique al remitente.



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